Topological Feature Extraction and Visualization of Whole Slide Images using Graph Neural Networks.
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Whole-slide images (WSI) are digitized representations of thin sections of stained tissue from various patient sources (biopsy, resection, exfoliation, fluid) and often exceed 100,000 pixels in any given spatial dimension. Deep learning approaches to digital pathology typically extract information from sub-images (patches) and treat the sub-images as independent entities, ignoring contributing information from vital large-scale architectural relationships. Modeling approaches that can capture higher-order dependencies between neighborhoods of tissue patches have demonstrated the potential to improve predictive accuracy while capturing the most essential slide-level information for prognosis, diagnosis and integration with other omics modalities. Here, we review two promising methods for capturing macro and micro architecture of histology images, Graph Neural Networks, which contextualize patch level information from their neighbors through message passing, and Topological Data Analysis, which distills contextual information into its essential components. We introduce a modeling framework, WSI-GTFE that integrates these two approaches in order to identify and quantify key pathogenic information pathways. To demonstrate a simple use case, we utilize these topological methods to develop a tumor invasion score to stage colon cancer.


Spatial Transcriptomics

MeSH terms

Computational Biology
Neural Networks, Computer


Levy, Joshua
Haudenschild, Christian
Barwick, Clark
Christensen, Brock
Vaickus, Louis

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